B. pertussis infects the upper respiratory tract by adhering to ciliated epithelial cells and releasing toxins. The virulence genes that encode these proteins are regulated by the BvgS-BvgA two-component system. The response regulator BvgA binds to the promoter region of all known B. pertussis virulence genes to activate their transcription during infection. These genes include bipA, fha, ptx, prn, cya, bvgR, bvgA, and the fim genes. B. pertussis adhesin and adhesin-related genes, such as fim2, fim3, and fimX, are among the earliest genes activated by BvgA upon its induction. The Fim proteins facilitate adhesion of the bacterium to epithelial cells in the human respiratory tract. During transcription, the sigma subunit of RNA polymerase (RNAP) is the specificity factor that recognizes promoter elements. Primary sigmas like E. coli sigma70 and B. pertussis sigma A have specific regions that contact promoter sequences. Residues within Regions 4, 3, and 2 interact with the -35 element, the extended -10 sequence (positions -15, -14), and the -10 element, respectively. The fim3 promoter (Pfim3) has both the sigma70-dependent extended -10 sequence and a -10 element, while the fim2 promoter (Pfim2) has only a canonical -10 sequence. Even though neither Pfim2 nor Pfim3 contains a recognizable -35 element, our previous results have indicated that the -35 region of Pfim3 accommodates sigma Region 4 as well as a phosphorylated BvgA and an alpha CTD. Using molecular modeling, we have determined how BvgA, sigma Region 4, and alpha might coexist within this DNA in a conformation that suggests a novel mechanism of activation. In a collaboration with the lab of S. Stibitz (FDA) we have examined in detail BvgA activation of transcription from Pfim3 and PfhaB, and we have reviewed the action of the B. pertussis response regulator BvgA in the context of what is known about bacterial RNA polymerase and various modes of transcription activation. At most virulence gene promoters, multiple dimers of phosphorylated BvgA bind upstream of the core promoter sequence, using a combination of high- and low-affinity sites that fill through cooperativity. Activation by phosphorylated BvgA is typically mediated by a novel form of Class I/II mechanisms, but two virulence genes, fim2 and fim3, which encode serologically distinct fimbrial subunits, are regulated using a previously unrecognized RNA polymerase/activator architecture. In addition, the fim genes undergo phase variation because of an extended cytosine (C) tract within the promoter sequences that is subject to slipped-strand mispairing during replication. These sophisticated systems of regulation demonstrate one aspect whereby B. pertussis, which is highly clonal and lacks the extensive genetic diversity observed in many other bacterial pathogens, has been highly successful as an obligate human pathogen.